Visualizing ’omic feature rankings and log-ratios using Qurro
| Autor: | Clarisse Marotz, Rob Knight, Eric E. Allen, Antonio Gonzalez, Cameron Martino, Gibraan Rahman, James T. Morton, Jeremiah J. Minich, Marcus W. Fedarko |
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| Rok vydání: | 2020 |
| Předmět: |
0303 health sciences
Point (typography) Biplot Application Notes 030306 microbiology Interface (Java) Computer science Rank (computer programming) Variation (game tree) computer.software_genre Plot (graphics) 03 medical and health sciences Feature (computer vision) sort Data mining computer 030304 developmental biology |
| Zdroj: | Nar Genomics and Bioinformatics |
| ISSN: | 2631-9268 |
| Popis: | Many tools for dealing with compositional ‘ ’omics’ data produce feature-wise values that can be ranked in order to describe features’ associations with some sort of variation. These values include differentials (which describe features’ associations with specified covariates) and feature loadings (which describe features’ associations with variation along a given axis in a biplot). Although prior work has discussed the use of these ‘rankings’ as a starting point for exploring the log-ratios of particularly high- or low-ranked features, such exploratory analyses have previously been done using custom code to visualize feature rankings and the log-ratios of interest. This approach is laborious, prone to errors and raises questions about reproducibility. To address these problems we introduce Qurro, a tool that interactively visualizes a plot of feature rankings (a ‘rank plot’) alongside a plot of selected features’ log-ratios within samples (a ‘sample plot’). Qurro’s interface includes various controls that allow users to select features from along the rank plot to compute a log-ratio; this action updates both the rank plot (through highlighting selected features) and the sample plot (through displaying the current log-ratios of samples). Here, we demonstrate how this unique interface helps users explore feature rankings and log-ratios simply and effectively. |
| Databáze: | OpenAIRE |
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